+Open data
-Basic information
Entry | Database: PDB / ID: 8cnk | ||||||
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Title | Cryo-EM structure of retinal-free proteoopsin bound to decanoate | ||||||
Components | Green-light absorbing proteorhodopsin | ||||||
Keywords | PROTON TRANSPORT / Membrane protein / Light-driven proton pump / Proteorhodopsin / Proteoopsin | ||||||
Function / homology | Function and homology information light-activated monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane Similarity search - Function | ||||||
Biological species | uncultured Gammaproteobacteria bacterium (environmental samples) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | ||||||
Authors | Hirschi, S. / Lemmin, T. / Fotiadis, D. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Structural insights into proteorhodopsin biogenesis and retinal scavenging Authors: Hirschi, S. / Lemmin, T. / Ayoub, N. / Kalbermatter, D. / Pellegata, D. / Ucurum, Z. / Gertsch, J. / Fotiadis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cnk.cif.gz | 197.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cnk.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cnk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8cnk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8cnk_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 8cnk_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/8cnk ftp://data.pdbj.org/pub/pdb/validation_reports/cn/8cnk | HTTPS FTP |
-Related structure data
Related structure data | 16759MC 8cqcC 8cqdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 26359.627 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured Gammaproteobacteria bacterium (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: Q6J4G7 #2: Chemical | ChemComp-DKA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pentameric proteoopsin bound to decanoate / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: uncultured Gammaproteobacteria bacterium (environmental samples) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 49.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 947286 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||
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